ive recently been downloading TONS of apps for my ipod touch (8gb gen 3)
i think i hit the limit of pages for it because i had a full 10 pages of apps, then i bought a new app for .99$ and it didnt show up due to my amount of pages :S
i can still use the app but only if i search it... i couldnt fix it in itunes

Yeah, the iPod Touch/iPhone is limited to 10 custom pages of apps.
The only way to get access to your new apps will be available through the search function.
How to delete apps on an iPod Touch:
1) Tap and hold any app
2) wait until the icons wiggle
3) press the red "x" to delete the app

Then you'll have to re-transfer your app that wasn't showing, but you also have to make sure the older app(s) aren't being synchronized again either.